PLA2R1

phospholipase A2 receptor 1, the group of C-type lectin domain containing

Basic information

Region (hg38): 2:159932005-160062615

Links

ENSG00000153246 ∙ ∙ OMIM:604939 ∙ HGNC:9042 ∙ Uniprot:Q13018 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLA2R1 gene.

• Inborn genetic diseases (44 variants)
• Kidney disorder (9 variants)
• not provided (4 variants)
• Atypical hemolytic-uremic syndrome (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2R1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	4		5
missense			42	5	4	51
nonsense						0
start loss						0
frameshift			1		1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	44	10	5

Variants in PLA2R1

This is a list of pathogenic ClinVar variants found in the PLA2R1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-159941788-C-G		not specified	Uncertain significance (Sep 26, 2023)
2-159942156-A-C		not specified	Uncertain significance (Nov 18, 2022)
2-159944947-G-A		not specified	Uncertain significance (Jul 13, 2021)
2-159944996-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-159945014-T-C		not specified	Uncertain significance (Feb 03, 2022)
2-159945031-C-A		not specified	Uncertain significance (Apr 26, 2023)
2-159945073-A-G		not specified	Uncertain significance (Nov 10, 2022)
2-159945074-T-G		not specified	Uncertain significance (Apr 22, 2022)
2-159946906-AAAGAT-A		Kidney disorder	Uncertain significance (Feb 01, 2018)
2-159949647-C-T		not specified	Uncertain significance (Dec 09, 2023)
2-159949672-G-A			Likely benign (Sep 01, 2022)
2-159949689-C-T		not specified	Uncertain significance (Jul 09, 2021)
2-159949706-G-A		not specified	Uncertain significance (Apr 12, 2022)
2-159949706-G-C		not specified	Uncertain significance (Jan 27, 2022)
2-159949747-G-A		Kidney disorder	Uncertain significance (Dec 12, 2016)
2-159951444-T-C		not specified	Uncertain significance (Jun 26, 2023)
2-159951479-G-C		not specified	Uncertain significance (May 31, 2023)
2-159951564-C-T		Atypical hemolytic-uremic syndrome	Benign (Oct 05, 2022)
2-159951566-T-C		not specified	Likely benign (Dec 13, 2022)
2-159955228-C-T		not specified	Uncertain significance (Mar 24, 2023)
2-159955235-T-C		not specified	Uncertain significance (Nov 17, 2023)
2-159955784-T-C		not specified	Uncertain significance (Aug 08, 2023)
2-159955814-T-A		not specified	Uncertain significance (Jan 03, 2024)
2-159956524-C-T		not specified	Likely benign (Jul 20, 2022)
2-159956530-A-G		not specified	Uncertain significance (Oct 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2R1	protein_coding	protein_coding	ENST00000283243	30	130603

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.23e-30	0.654	122849	78	2821	125748	0.0116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.351	748	775	0.965	0.0000394	9724
Missense in Polyphen		241	271.33	0.88822		3606
Synonymous	0.394	263	271	0.970	0.0000144	2564
Loss of Function	2.57	60	85.7	0.700	0.00000400	1012

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.119	0.118
Ashkenazi Jewish	0.0484	0.0484
East Asian	0.000666	0.000653
Finnish	0.00106	0.00106
European (Non-Finnish)	0.00249	0.00246
Middle Eastern	0.000666	0.000653
South Asian	0.00250	0.00249
Other	0.0120	0.0118

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for secretory phospholipase A2 (sPLA2). Acts as a receptor for phosholipase sPLA2-IB/PLA2G1B but not sPLA2- IIA/PLA2G2A. Also able to bind to snake PA2-like toxins. Although its precise function remains unclear, binding of sPLA2 to its receptor participates in both positive and negative regulation of sPLA2 functions as well as clearance of sPLA2. Binding of sPLA2- IB/PLA2G1B induces various effects depending on the cell type, such as activation of the mitogen-activated protein kinase (MAPK) cascade to induce cell proliferation, the production of lipid mediators, selective release of arachidonic acid in bone marrow- derived mast cells. In neutrophils, binding of sPLA2-IB/PLA2G1B can activate p38 MAPK to stimulate elastase release and cell adhesion. May be involved in responses in proinflammatory cytokine productions during endotoxic shock. Also has endocytic properties and rapidly internalizes sPLA2 ligands, which is particularly important for the clearance of extracellular sPLA2s to protect their potent enzymatic activities. The soluble secretory phospholipase A2 receptor form is circulating and acts as a negative regulator of sPLA2 functions by blocking the biological functions of sPLA2-IB/PLA2G1B. {ECO:0000269|PubMed:15611272, ECO:0000269|PubMed:7721806}.
• Pathway: Phagosome - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Acyl chain remodelling of PI;Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;Acyl chain remodelling of PC;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE;Synthesis of PA (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.999
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.64

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.399
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.157

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pla2r1
• Phenotype: immune system phenotype

Gene ontology

• Biological process: cytokine production;receptor-mediated endocytosis;positive regulation of DNA damage response, signal transduction by p53 class mediator;reactive oxygen species metabolic process;positive regulation of arachidonic acid secretion;replicative senescence;oxidative stress-induced premature senescence;negative regulation of phospholipase A2 activity;negative regulation of arachidonic acid secretion
• Cellular component: extracellular region;plasma membrane;cell surface;integral component of membrane;receptor complex
• Molecular function: transmembrane signaling receptor activity;carbohydrate binding;phospholipase binding